Evaluation of Fourier Transform Infrared Spectroscopy as a First-Line Typing Tool for the Identification of Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae Outbreaks in the Hospital Setting

Jun Hao Wang-Wang; Antoni E Bordoy; Elisa Martró; María Dolores Quesada; María Pérez-Vázquez; Mercedes Guerrero-Murillo; Andrea Tiburcio; Marina Navarro; Laia Castellà; Nieves Sopena; Irma Casas; Verónica Saludes; Montserrat Giménez; Pere-Joan Cardona

doi:10.3389/fmicb.2022.897161

Evaluation of Fourier Transform Infrared Spectroscopy as a First-Line Typing Tool for the Identification of Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae Outbreaks in the Hospital Setting

Front Microbiol. 2022 Jun 9:13:897161. doi: 10.3389/fmicb.2022.897161. eCollection 2022.

Authors

Jun Hao Wang-Wang^{1

2}, Antoni E Bordoy^{1

3}, Elisa Martró^{1

2

3

4}, María Dolores Quesada^{1

2

4}, María Pérez-Vázquez^{5

6}, Mercedes Guerrero-Murillo^{7

8}, Andrea Tiburcio¹, Marina Navarro¹, Laia Castellà⁹, Nieves Sopena¹⁰, Irma Casas¹¹, Verónica Saludes^{1

2

3

4}, Montserrat Giménez^{1

4}, Pere-Joan Cardona^{1

2

3

12}

Affiliations

¹ Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain.
² Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Bellaterra, Spain.
³ Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
⁴ Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
⁵ Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
⁶ Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
⁷ Clinical Genomics Research Unit, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Badalona, Spain.
⁸ Clinical Genomics Unit, Clinical Genetics Service, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Can Ruti Campus, Badalona, Spain.
⁹ Enfermería Control de Infección, Dirección Enfermería, Germans Trias i Pujol University Hospital, Badalona, Spain.
¹⁰ Infectious Diseases Department, Germans Trias i Pujol University Hospital, Badalona, Spain.
¹¹ Preventive Medicine Department, Germans Trias i Pujol University Hospital, Badalona, Spain.
¹² Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.

Abstract

Early detection of pathogen cross-transmission events and environmental reservoirs is needed to control derived nosocomial outbreaks. Whole-genome sequencing (WGS) is considered the gold standard for outbreak confirmation, but, in most cases, it is time-consuming and has elevated costs. Consequently, the timely incorporation of WGS results to conventional epidemiology (CE) investigations for rapid outbreak detection is scarce. Fourier transform infrared spectroscopy (FTIR) is a rapid technique that establishes similarity among bacteria based on the comparison of infrared light absorption patterns of bacterial polysaccharides and has been used as a typing tool in recent studies. The aim of the present study was to evaluate the performance of the FTIR as a first-line typing tool for the identification of extended-spectrum β-lactamase-producing Klebsiella pneumoniae (ESBL-Kp) outbreaks in the hospital setting in comparison with CE investigations using WGS as the gold standard method. Sixty-three isolates of ESBL-Kp collected from 2018 to 2021 and classified according to CE were typed by both FTIR and WGS. Concordance was measured using the Adjusted Rand index (AR) and the Adjusted Wallace coefficient (AW) for both CE and FTIR clustering considering WGS as the reference method. Both AR and AW were significantly higher for FTIR clustering than CE clustering (0.475 vs. 0.134, p = 0.01, and 0.521 vs. 0.134, p = 0.009, respectively). Accordingly, FTIR inferred more true clustering relationships than CE (38/42 vs. 24/42, p = 0.001). However, a similar proportion of genomic singletons was detected by both FTIR and CE (13/21 vs. 12/21, p = 1). This study demonstrates the utility of the FTIR method as a quick, low-cost, first-line tool for the detection of ESBL-Kp outbreaks, while WGS analyses are being performed for outbreak confirmation and isolate characterization. Thus, clinical microbiology laboratories would benefit from integrating the FTIR method into CE investigations for infection control measures in the hospital setting.

Keywords: FTIR; Fourier transform infrared spectroscopy; Klebsiella pneumoniae; cluster analysis; conventional epidemiology; nosocomial infection; outbreak; whole-genome sequencing.